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Spatially varying water-level regimes are a factor controlling estuarine and tidal-fluvial wetland vegetation patterns. As described in Part I, water levels in the Lower Columbia River and estuary (LCRE) are influenced by tides, river flow, hydropower operations, and coastal processes. In Part II, regression models based on tidal theory are used to quantify the role of these processes in determining water levels in the mainstem river and floodplain wetlands, and to provide 21-year inundation hindcasts. Analyses are conducted at 19 LCRE mainstem channel stations and 23 tidally exposed floodplain wetland stations. Sum exceedance values (SEVs) are used to compare wetland hydrologic regimes at different locations on the river floodplain. A new predictive tool is introduced and validated, the potential SEV (pSEV), which can reduce the need for extensive new data collection in wetland restoration planning. Models of water levels and inundation frequency distinguish four zones encompassing eight reaches. The system zones are the wave-and current-dominated Entrance to river kilometer (rkm) 5; the Estuary (rkm-5 to 87), comprised of a lower reach with salinity, the energy minimum (where the turbidity maximum normally occurs), and an upper estuary reach without salinity; the Tidal River (rkm-87 to 229), with lower, middle, and upper reaches in which river flow becomes increasingly dominant over tides in determining water levels; and the steep and weakly tidal Cascade (rkm-229 to 234) immediately downstream from Bonneville Dam. The same zonation is seen in the water levels of floodplain stations, with considerable modification of tidal properties. The system zones and reaches defined here reflect geological features and their boundaries are congruent with five wetland vegetation zones.

We describe the changes in the floral assemblage in a salt marsh after reconnection to estuarine tidal inundation. The Elk River marsh in Grays Harbor, Washington was opened to tidal flushing in 1987 after being diked for approximately 70 years. The freshwater pasture assemblage dominated by Phalarais arundinacea (reed canary grass) converted to low salt marsh vegetation within 5 years, with the major flux in species occurring between years 1 and 4. The system continued to develop through the 11-year post-breach monitoring period, although change after year 6 was slower than in previous years. The assemblage resembles a low salt marsh community dominated by Distichlis spicata (salt grass) and Salicornia virginica (pickleweed). Because of subsidence of the system during the period of breaching, the restored system remains substantially different from the Deschamsia cespitosa (tufted hairgrass)-dominated reference marsh. Use of a similarity index to compare between years and also between reference and restored marshes in the same year revealed that similarity in floral composition between year 0 and subsequent years decreased with time. However, there was a period of dramatic dissimilarity during years 1 to 3 when the system was rapidly changing from a freshwater to estuarine condition.Similarity values between the reference and restored system generally increased with time. Somewhat surprisingly the reference marsh showed considerable between-year variation in similarity, which indicated substantial year-to-year variability in species composition. Based on accretion rate data from previous studies we predict that full recovery of the system would take between 75 and 150 years.

We developed light requirements for eelgrass in the Pacific Northwest, USA, to evaluate the effects of shortand long-term reductions in irradiance reaching eelgrass, especially related to turbidity and overwater structures. Photosynthesis-irradiance experiments and depth distribution field studies indicated that eelgrass productivity was maximum at a photosynthetic photon flux density (PPFD) of about 350-550 μmol quanta m −2 s −1 . Winter plants had approximately threefold greater net apparent primary productivity rate at the same irradiance as summer plants.Growth studies using artificial shading as well as field monitoring of light and eelgrass growth indicated that longterm survival required at least 3 mol quanta m −2 day −1 on average during spring and summer (i.e., May-September), and that growth was saturated above about 7 mol quanta m −2 day −1 . We conclude that non-light-limited growth of eelgrass in the Pacific Northwest requires an average of at least 7 mol quanta m −2 day −1 during spring and summer and that long-term survival requires a minimum average of 3 mol quanta m −2 day −1 .

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The research presented in this report is part of the regional habitat restoration program in the lower Columbia River and estuary (LCRE). As part of this program, we have established a suite of reference sites to help meet the goal of understanding and restoring wetland habitat. The data collected at these reference sites from 2005 through the present were analyzed in this study to meet two primary objectives: 1) to inform restoration planning and design by quantifying the ecological and hydrological conditions necessary for development of wetland plant communities and tidal channel networks and 2) to evaluate the effectiveness of wetland restoration actions in the LCRE by comparing restoration and reference site monitoring data. In this report, we present the results of the analysis of 51 reference wetland sites, focusing on the elevation, sediment, and inundation ranges required by native tidal wetland vegetation. We describe critical factors influencing existing wetland patterns in the LCRE, including the vegetation assemblages present, the elevation ranges at which they occur, and the inundation dynamics that result in their current distribution. Finally, we present how these data can be used to evaluate restoration action effectiveness. v Executive Summary vi Hydro-Vegetation Zones Shallow-water vegetation assemblages show distinct differences along the gradient between the mouth of the river and the upstream end of the estuary at Bonneville Lock and Dam. There are three zones based on species richness; the central region (rkm 50 to rkm 150) has the greatest number of species, and the upper and lower ends of the estuary have lower numbers of species. These three species richness zones can be characterized hydrodynamically as tidal-dominated, mixed tidal and riverdominated, and river-dominated, moving from the mouth of the Columbia River to Bonneville Dam. We hypothesize that fewer vegetation species are physiologically adapted to the extreme inundation in the upper end of the estuary, and, likewise, few are adapted to the tidal variability and salinity in the lower estuary. The fact that the mixed zone contains the greatest number of species suggests that the natural ecological disturbance regime may be lower there, and there may be a larger species pool adapted for these conditions in this zone. This intermediate disturbance hypothesis has been used in many ecosystems to describe the conditions that result in higher species diversity. Further examination of the hydrologic gradient revealed that the estuary can be divided further into five zones, driven primarily by salinity intrusion at the lower end and stronger fluvial flooding influence at the upper end. The breaks for these zones occur at approximately rkm 40, 104, 136, and 181. These breaks are preliminary and should be refined with additional data in areas of sparse sites and with other hydrologic analyses currently under way. The five hydro-vegetation zones developed from this analysis provide a means of determining the ranges of controlling factors ...

Protocols for Monitoring Habitat Restoration Projects in the Lower Columbia River and Estuaryiii AbstractThis document describes a set of protocols developed by the National Marine Fisheries Service of the National Oceanographic and Atmospheric Administration, Pacific Northwest National Laboratory, and the Columbia River Estuary Study Taskforce with the support of the U.S. Army Corps of Engineers. These protocols are designed for researchers and managers monitoring the effectiveness of actions to restore degraded wetland habitat in the lower Columbia River and estuary (CRE). The intent is to promote a standard set of monitoring protocols to assess and compare habitat restoration projects in the region.The goal of many restoration activities in the CRE is to repair the connectivity and function of wetland habitats, and thereby to allow juvenile salmon to regain benefit from these important rearing and refuge areas. To do this effectively, researchers and managers require the means to 1) evaluate the results of individual restoration activities, 2) compare results among projects, and 3) determine the long-term and cumulative effects of habitat restoration on the overall estuary ecosystem. To help achieve this, we have developed a standardized set of monitoring protocols. We limited the number of metrics to a proposed "core" set and selected measurement methods that are straightforward and economical to use. By "core," we mean an optimum suite of metrics that can adequately detail the results of restoration, depending on the goals of the restoration action and financial and logistical limitations of comprehensively monitoring ecological change over extended temporal and spatial scales. We selected core metrics based on the following criteria: 1) correspond to commonly held restoration project goals; 2) are applicable to all sites; 3) characterize controlling factors, ecosystem structure, and ecosystem function; 4) are relevant to both present and future investigations; and 5) are practical in terms of level of effort.In this document, we summarize the types of restoration strategies being planned and implemented in the CRE. We then propose a set of metrics and statistical design for restoration monitoring activities based on commonly shared ecological goals. Finally, we provide specific protocols for this set of estuary monitoring metrics. Monitoring protocols are provided for hydrology (water surface elevation); water quality (temperature, salinity); elevation (topography); landscape features (remote sensing); plant community (composition and cover); vegetation plantings (success); and fish community (species, temporal presence, size/age structure).

Abstract. This study adapts and applies the evidence-based approach for causal inference, a medical standard, to the restoration and sustainable management of large-scale aquatic ecosystems. Despite long-term investments in restoring aquatic ecosystems, it has proven difficult to adequately synthesize and evaluate program outcomes, and no standard method has been adopted. Complex linkages between restorative actions and ecosystem responses at a landscape scale make evaluations problematic and most programs focus on monitoring and analysis. Herein, we demonstrate a new transdisciplinary approach integrating techniques from evidence-based medicine, critical thinking, and cumulative effects assessment. Tiered hypotheses about the effects of landscape-scale restorative actions are identified using an ecosystem conceptual model. The systematic literature review, a health sciences standard since the 1960s, becomes just one of seven lines of evidence assessed collectively, using critical thinking strategies, causal criteria, and cumulative effects categories. As a demonstration, we analyzed data from 166 locations on the Columbia River and estuary representing 12 indicators of habitat and fish response to floodplain restoration actions intended to benefit culturally and economically important, threatened and endangered salmon. Synthesis of the lines of evidence demonstrated that hydrologic reconnection promoted macrodetritis export, prey availability, and juvenile fish access and feeding. Upon evaluation, the evidence was sufficient to infer cross-boundary, indirect, compounding, and delayed cumulative effects, and suggestive of nonlinear, landscape-scale, and spatial density effects. Therefore, on the basis of causal inferences regarding foodweb functions, we concluded that the restoration program is having a cumulative beneficial effect on juvenile salmon. The lines of evidence developed are transferable to other ecosystems: modeling of cumulative net ecosystem improvement, physical modeling of ecosystem controlling factors, meta-analysis of restoration action effectiveness, analysis of data on target species, research on critical ecological uncertainties, evidence-based review of the literature, and change analysis on the landscape setting. As with medicine, the science of ecological restoration needs scientific approaches to management decisions, particularly because the consequences affect species extinctions and the availability of ecosystem services. This evidencebased approach will enable restoration in complex coastal, riverine, and tidal-fluvial ecosystems like the lower Columbia River to be evaluated when data have accumulated without sufficient synthesis.